Pooled Libraries
Addgene depositors have shared 390 pooled libraries — tens to millions of plasmids in a single tube all built with the same backbone and only differing in a small region. Find pooled libraries for barcoding, CRISPR, screening, and surface display experiments below.
Barcoding Libraries
Barcode libraries contain large numbers of plasmids, each with a short randomized unique nucleotide sequence, or barcode used to mark individual cells. These barcodes will then be inherited by any daughter cells, making barcode libraries ideal for lineage tracing. These libraries are also commonly used to monitor the dynamics of heterogeneous tumors.
| ID | Library | Description | Vector Type | # of Barcodes | Fluorescent Reporter | Selectable Marker | PI | |
|---|---|---|---|---|---|---|---|---|
| 180483 186334 186335 |
STICR Library | Used for labeling a starting cell population and for clonal lineage/fate tracing. | Lentiviral | ~50–70 million | EGFP | N/A | Tomasz Nowakowski | |
| 155257 | Watermelon Library | Used for simultaneous tracing of clonal lineages as well as the transcriptional and proliferative state of each cell in the population. | Lentiviral | 5×106 | mCherry, mNeonGreen | N/A | Aviv Regev, Joan Brugge | |
| 194097 194098 217420 217421 217422 217423 217424 1000000239 |
Single-cell quantitative expression reporters (scQers) Libraries | Used for integrating your regulatory elements of interest for single-cell expression reporter assays. | Mammalian Expression | ~1,200,000 ~1,200,000 250 250 250 250 250 1,250 |
N/A EGFP EGFP EGFP EGFP EGFP EGFP EGFP |
N/A N/A Puromycin Puromycin Puromycin Puromycin Puromycin Puromycin |
Jay Shendure | |
| 179774 179775 179776 |
SPLINTR Pooled Libraries | Used for tracing clonal lineages using bulk and single-cell readouts. | Lentiviral | 170,000 1.3 million 670,000 |
EGFP mCherry EBFP2 |
N/A | Mark Dawson | |
| 140024 | LARRY Barcode Library Version 1 (Discontinued) | Used for reconstructing transcriptional trajectories and clonal and state-fate analyses in differentiating cell populations. | Lentiviral | 245,979 | EGFP | N/A | Fernando Camargo | |
| 233213 233214 233215 233216 233697 |
LARRY Barcode Library Version 2 | Used for reconstructing transcriptional trajectories and clonal and state-fate analyses in differentiating cell populations. | Lentiviral | >50 million | T-Sapphire T-Sapphire EGFP EGFP mScarlet |
N/A | Alejo Rodriguez-Fraticelli | |
| 178943 | macsGESTALT Library | PiggyBac barcoding library for inducible lineage recording system. | Mammalian Expression | theoretically >1 million | N/A | Puromycin | Christopher Lengner | |
| 179851 179852 |
Moffat Lab - Barcode Libraries | Library with Puromycin and ZsGreen markers. | Lentiviral | >106 | ZsGreen | Puromycin | Jason Moffat | |
| 67267 69830 |
ClonTracer Library | Used to conduct positive selection screens for cancer cells resistant to a given treatment. Learn how the library was used to identify pools of cells that were resistant pre-treatment. | Lentiviral | ~73 million | TagRFP | Puromycin | Frank Stegmeier | |
| 115643 115644 115645 206045 |
CellTag Barcode Library | Used to combinatorially index cells for single-cell analysis of clonal dynamics. Available as a viral prep. | Lentiviral | 19,973 4,934 5,737 ~80,000 |
EGFP | N/A | Samantha Morris | |
| 85968 | Perturb-seq Guide Barcodes (GBC) Library | Used for cloning gRNA sublibraries for single cell CRISPR analysis. | Lentiviral | >100,000 | TagBFP | Puromycin | Jonathan Weissman | |
| 170392 | Target Site Library (PCT48) | Library backbone contains three Cas9-targetable spacer sequences with a random 14-bp barcode. | Lentiviral | theoretically >100 million | sfGFP | Puromycin | Jonathan Weissman | |
| 229136 | EGFP miSFIT Lineage Barcoding Library | Create a lentiviral barcoding pool that is robustly expressed in human PSC-derived hematopoietic cells. | Lentiviral | >500,000 | EGFP | N/A | Peter Zandstra | |
| 238546 238547 238548 |
PEtracer Lentiviral Libraries | Libraries containing selectable markers that encode ground truth static marks for phylogenetic reconstructions. | Lentiviral | ~100,000–150,000 ~100,000–150,000 2,170 |
N/A N/A mCherry |
Puromycin Blasticidin N/A |
Jonathan Weissman | |
| 227193 | pMuSIC pool v1.0 | Fluorescent barcoding library with 153 unique fluorescent protein barcodes made from 2-way combinations of 18 individual fluorescent proteins. | Mammalian Expression | 153 | Multiple | N/A | Marc Birtwistle | |
| 211610 | PolyA Barcode Library | Retroviral barcoding library for capturing the transcriptome and cell identities. | Retroviral | >3 million | EGFP | N/A | Yuejun Chen | |
| 232068 | CRASP-Seq CBC Backbone Library | Used for cloning custom libraries tailored to CRASP-Seq modulation approaches. A 12-nucleotide cell barcode enables library diversification for downstream cloning. | Lentiviral | >107 | N/A | Puromycin | Thomas Gonatopoulos-Pournatzis | |
| 216133 216134 |
Human Genome-wide Intron Tagging Libraries | Intron-targeting sgRNAs for pooled tagging of proteins with GFP or other protein tags at their endogenous genomic locus using an intron tagging approach. | Lentiviral | 90,657 sgRNAs, 1,000 control 72,580 sgRNAs, 1,000 control |
N/A | Puromycin Blasticidin |
Stefan Kubicek | |
| 227671 227672 | Rabies Barcode Pooled Libraries | G-deleted rabies virus barcoding libraries for neuronal tracing and high-fidelity connectivity mapping. | G-deleted Rabies Virus | ~125,000,000 | dTomato oScarlet |
N/A | Tomasz Nowakowski, Cathryn Cadwell |
CRISPR Pooled Libraries
CRISPR is a useful tool for genetic screening experiments, due to the relative ease of designing gRNAs and the ability to modify virtually any genetic locus. CRISPR pooled libraries deliver many gRNAs at once, targeting many genes in one experiment. These libraries may be designed to target all the genes in the genome of an organism or a subset of genes, such as those involved in a certain pathway or biological process. In a CRISPR screening experiment, target cells are treated with the pooled library to create a population of mutant cells that are then screened for a phenotype of interest. Screening experiments using a pooled CRISPR library are far more complex than using CRISPR to modify a single genomic locus. You can learn more about CRISPR-based gene regulation on our CRISPR Guide.
There are multiple types of CRISPR libraries:
- Knockout: CRISPR knockout libraries are designed to create insertions or deletions in targeted genes across the genome, rendering them nonfunctional.
- Activation: CRISPR activation libraries use gRNAs to guide dCas9 bound to a transcriptional activator to target genes and thereby activate their expression.
- Inhibition: CRISPR inhibition libraries use gRNAs to guide dCas9 bound to a transcriptional repressor to target genes, block transcription initiation, and thereby repress, or knockdown, their expression.
- Base Edit: CRISPR base edit libraries use gRNAs to guide base editors to convert one base to another.
- Prime Edit: CRISPR prime edit libraries use prime editing guide RNAs (pegRNAs) to target genes for creating insertions, deletions, and base edits.
- Other: CRISPR libraries have also been designed for other specific purposes, such as barcoding or targeting RNA.
When choosing your library, please be aware that some of the library vectors contain Cas enzyme (one-plasmid system), while others require co-infection with Cas enzyme-expressing virus or use in cells expressing Cas enzyme (two-plasmid system).
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Screening Libraries
Screening libraries (non-CRISPR) can be used for different types of high-throughput experiments, including studying regulatory sequences, screening certain types of proteins (such as cell surface receptors or transcription factors), or observing the effects of mutagenesis of a single gene.
| ID | Library | Description | Species | Vector Type | Selection Marker | PI | |
|---|---|---|---|---|---|---|---|
| 1000000214 | APA Variant and Reference Libraries | Libraries made to experimentally validate a residual neural network model's (APARENT2) predictions for 3′-cleavage and polyadenylation from DNA sequence. | Human | Mammalian Expression | N/A | Georg Seelig | |
| 243681 243682 |
attB GPCR Libraries | Libraries for stable recombination of nearly all human human G protein-coupled receptors (GPCRs) with unique molecular identifiers (UMIs). | Human | Cloning | GFP | Jonathan Schlebach | |
| 172109 | Cancer Driver Peptide Overexpression Library | Library expressing tiled cancer driver peptides for fitness screening. | Human | Lentiviral | Puromycin | Prashant Mali | |
| 208054 | Cultivarium MACKEREL Library | Golden Gate compatible library to study a broad host range of prokaryotic promoters-RBS regulatory sequences. | Bacteria | Bacterial Expression | Chloramphenicol | Nili Ostrov, Charlie Gilbert, Cultivarium Tools | |
| 1000000194 1000000195 1000000196 |
DHFR Saturation Mutagenesis Libraries | Libraries to study the interaction between dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. | E. coli | Bacterial Expression | Chloramphenicol | Kimberly Reynolds | |
| 160132 160133 160134 160135 |
High Throughput PAM Determination Assay Libraries | Libraries for determining the PAM requirements of Cas enzymes. | Synthetic | Reporter | Ampicillin | Keith Joung, Benjamin Kleinstiver | |
| 224585 | Ma-PylRS-lib1 Library | Pyrrolysine tRNA synthetase library to generate new genetic code expansion (GCE) systems for site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. | M. alvus | Bacterial Expression | Kanamycin | Ryan Mehl | |
201012 |
microTRE Screening Library | Libraries to screen synthetic promoters for transcriptional readouts of specific upstream signaling events. | Synthetic, but based on human and mouse | Reporter | N/A | Justin English | |
| 207474 207475 207476 207477 207478 207479 207480 207481 |
Modular Pooled Knockin Libraries | Libraries for screening transcription factors and cell surface receptors with a T cell receptor or chimeric antigen receptor for engineering immunotherapies and other cellular functions. | Human | Cloning/HDRT Generation | N/A | Alexander Marson | |
| 198050 | pCMV-Rep78/68 Scanning Saturation Mutagenesis (SSM) Library | Investigate the effects of rep mutations on production of a wide range of AAV capsid serotypes. | AAV2 | AAV | N/A | George Church | |
| 199601 | pRep-Cap Scanning Saturation Mutagenesis (SSM) Library | Investigate the effects of cap gene mutations on AAV production and on capsid properties. | AAV2 | AAV | N/A | George Church | |
| 1000000181 | PYR1 Double Mutant Library | Paired double mutant Pyrabactin Resistance 1 libraries. | A. thaliana | Yeast Expression | TRP1 | Timothy Whitehead | |
| 241288 241289 |
PYR1 Double-Hao and Triple Mutant Libraries | PYR1 receptor libraries to isolate sensors using growth-based selections in yeast. | Arabidopsis | Yeast Two Hybrid | TRP1 | Cutler | |
111704 |
Rinehart Human Serine Phosphopeptide Library | Human phosphoserine libraries. | Human | Bacterial Expression | Ampicillin | Jesse Rinehart | |
| 188526 188527 188528 188529 188530 188531 188532 188533 188534 188535 188536 1000000199 1000000200 1000000201 1000000202 1000000203 1000000204 1000000205 1000000206 1000000207 1000000208 1000000209 |
Rinehart Lab Iterative Synthetically Phosphorylated Isomers (iSPI) Library | New generation of human phosphoserine libraries. | Human | Bacterial Expression | Ampicillin | Jesse Rinehart | |
| 127842 | SPECS Library | Library for high-throughput screening for identification of synthetic promoters with enhanced cell-state specificity. | Synthetic | Lentiviral | N/A | Timothy Lu | |
| 213694 | Superti-Furga Human SLC Overexpression Library | An inducible barcoded overexpression library to test the impact of SLC transporters on biological processes. | Human | Lentiviral | Puromycin | Giulio Superti-Furga | |
| 1000000264 | TCR Rapid Assembly for Functional Testing (TCRAFT) Libraries | Use TCRAFT libraries for functional screening. | Human | Cloning | N/A | Michael Birnbaum | |
| 113569 | TP53 Mutagenesis Library | Designed for the characterization of all possible p53 mutations. | Human | Lentiviral | Puromycin | William Hahn, David Root | |
| 137000 192821 1000000218 |
Zhang Lab Multiplexed Overexpression of Regulatory Factors (MORF) Library | This pooled library of lentiviral plasmids expresses barcoded isoforms of human transcription factors. | Human | Lentivirus | Puromycin | Feng Zhang | |
| 79153 | Cas13a/C2c2 Protospacer flanking site (PFS) Library | A protospacer flanking site (PFS) library that can be used to evaluate Cas13a binding. | E. coli | Bacterial Expression | N/A | Feng Zhang |
Surface Display Libraries
Surface display is a genetic engineering technique that physically links a protein's function (phenotype) to the gene that encodes it (genotype). This is achieved by fusing the gene of interest with a gene for an anchoring protein. The resulting fusion protein is then expressed on the surface of a host cell or virus, such as bacteriophages or yeast.
The key advantage of this approach is the ability to screen large, diverse libraries for specific binding properties without the need to purify individual proteins. Any successful candidate can be readily identified by recovering and sequencing its associated genetic material.
Commonly used surface display platforms include:
- Phage Display: In this system, a peptide or protein is fused to a bacteriophage coat protein. The resulting phages can be screened for binding affinity to a target molecule.
- Yeast Display: In this system, proteins are displayed on the surface of Saccharomyces cerevisiae, often by fusion to the Aga2p protein. This platform supports the correct folding and post-translational modification of complex eukaryotic proteins, such as antibodies.
| ID | Library | Description | Species | Backbone Vector | PI | |
|---|---|---|---|---|---|---|
| 1000000071 | Synuclein VHH Immune Library | Created for research in Parkinson's disease; for target validation and drug design | Camelid | Phagemid | Anne Messer, MJFF | |
| 157971 157972 157973 168776 168777 174293 174294 174295 174296 |
SARS-CoV-2 Spike (S) Ectodomain and RBD Libraries | Libraries of Spike (S) Ectodomain and RBD mutants. | Coronavirus | Yeast surface display | Timothy Whitehead | |
| 1000000172 | SARS-CoV-2 Spike Receptor Binding Domain Deep Mutation Scanning Library | Library of Spike protein RBD mutations for comprehensive mapping. | Coronavirus | Yeast surface display | Jesse Bloom | |
| 1000000182 1000000183 1000000184 1000000185 1000000186 1000000187 1000000188 |
SARS-CoV-2 Spike Receptor Binding Domain Site-Saturation Mutagenesis Library | Libraries of variant Spike protein RBD mutations for comprehensive mapping. | Coronavirus | Yeast surface display | Jesse Bloom |
cDNA Libraries
cDNA libraries are created from an organism’s actively transcribed mRNA, as opposed to genomic libraries, which are created from genomic DNA. Since cDNA libraries lack introns and other nontranscribed sequences, they are smaller and easier to use than genomic libraries, but they do not contain as much regulatory information. To make a cDNA library, cDNA is synthesized, ligated to adapters, and then cloned into a given vector.
| ID | Library | Description | Species | PI | |
|---|---|---|---|---|---|
| 62843 | S. rosetta Col- cDNA amplified library | Created from the choanoflagellate Salpingoeca rosetta. Col- refers to DNA isolated from bacteria cultured with the colony-inducing bacteria Algoriphagus machipongonensis. | Salpingoeca rosetta | Nicole King | |
| 62844 | S. rosetta Col+ cDNA amplified library | Created from the choanoflagellate Salpingoeca rosetta. The Col+ library was created from S. rosetta cultured without bacteria. | Salpingoeca rosetta | Nicole King | |
| 25864 | Monosiga cDNA Library (Discontinued) |
Bacterial expression cDNA library created from the choanoflagellate Monosiga brevicollis. | Monosiga brevicollis | Sean Carroll, Nicole King | |
| 25716 | Proterospongia cDNA library (Discontinued) |
Bacterial expression cDNA library created from Proterospongia, also referred to as Salpingoeca. | Proterospongia | Nicole King |
shRNA Libraries
Addgene currently does not distribute any shRNA libraries. DECIPHER libraries below were previously distributed by Addgene and have been discontinued as of October 2016, but are noted here for historical reference.
| ID | Library | Species | Vector Type | Targets | Total shRNAs | PI | |
|---|---|---|---|---|---|---|---|
| 29589 | DECIPHER Mod 3: Cell Surface, etc. (Discontinued) |
Human | Lentiviral | 4,922 | 27,500 | Alex Chenchik | |
|
|
28285 28286 |
DECIPHER Mod 1: Pathway Targets (Discontinued) DECIPHER Mod 2: Disease Targets (Discontinued) |
Human | Lentiviral | 5,043 5,412 |
27,500 | Alex Chenchik, Gus Frango |
|
|
28287 28288 |
DECIPHER Mod 1: Pathway Targets (Discontinued) DECIPHER Mod 2: Disease Targets (Discontinued) |
Mouse | Lentiviral | 4,625 4,520 |
27,500 | Alex Chenchik, Gus Frango |
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Content last reviewed: 12 November 2025
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